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author | BioArchLinuxBot | 2023-09-04 18:06:46 +0000 |
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committer | BioArchLinuxBot | 2023-09-04 18:06:46 +0000 |
commit | d131baaf46c635901923b66fc36469eb33d14ad3 (patch) | |
tree | acf55f1f13c83d01cc98d242981b02a3ba1eab73 | |
parent | f6085d771e2ce88c13887f4a48c7cf54d32915c9 (diff) | |
download | aur-d131baaf46c635901923b66fc36469eb33d14ad3.tar.gz |
[lilac] updated to 1.26.0-4
-rw-r--r-- | .SRCINFO | 12 | ||||
-rw-r--r-- | PKGBUILD | 45 |
2 files changed, 36 insertions, 21 deletions
@@ -1,13 +1,15 @@ pkgbase = r-fgsea pkgdesc = Fast Gene Set Enrichment Analysis pkgver = 1.26.0 - pkgrel = 3 + pkgrel = 4 url = https://bioconductor.org/packages/fgsea arch = x86_64 license = MIT - depends = gcc - depends = r - depends = r-bh + checkdepends = r-geoquery + checkdepends = r-limma + checkdepends = r-reactome.db + checkdepends = r-testthat + makedepends = r-bh depends = r-biocparallel depends = r-cowplot depends = r-data.table @@ -22,12 +24,12 @@ pkgbase = r-fgsea optdepends = r-limma optdepends = r-msigdbr optdepends = r-org.mm.eg.db - optdepends = r-parallel optdepends = r-reactome.db optdepends = r-rmarkdown optdepends = r-seurat optdepends = r-testthat source = https://bioconductor.org/packages/release/bioc/src/contrib/fgsea_1.26.0.tar.gz + md5sums = 3b02276027800535421f38bbe5e83921 sha256sums = ffd44dcf4e4a757ae4c79f3df99897a3e126fbca3e54457ace2c8cc923cf1632 pkgname = r-fgsea @@ -1,19 +1,16 @@ -# system requirements: C++11 -# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net> +# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com> +# Contributor: Guoyi Zhang <guoyizhang at malacology dot net> _pkgname=fgsea _pkgver=1.26.0 pkgname=r-${_pkgname,,} -pkgver=1.26.0 -pkgrel=3 -pkgdesc='Fast Gene Set Enrichment Analysis' -arch=('x86_64') +pkgver=${_pkgver//-/.} +pkgrel=4 +pkgdesc="Fast Gene Set Enrichment Analysis" +arch=(x86_64) url="https://bioconductor.org/packages/${_pkgname}" -license=('MIT') +license=(MIT) depends=( - gcc - r - r-bh r-biocparallel r-cowplot r-data.table @@ -22,6 +19,15 @@ depends=( r-rcpp r-scales ) +makedepends=( + r-bh +) +checkdepends=( + r-geoquery + r-limma + r-reactome.db + r-testthat +) optdepends=( r-aggregation r-annotationdbi @@ -30,22 +36,29 @@ optdepends=( r-limma r-msigdbr r-org.mm.eg.db - r-parallel r-reactome.db r-rmarkdown r-seurat r-testthat ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('3b02276027800535421f38bbe5e83921') sha256sums=('ffd44dcf4e4a757ae4c79f3df99897a3e126fbca3e54457ace2c8cc923cf1632') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_pkgname}/LICENCE" -t "${pkgdir}/usr/share/licenses/${pkgname}" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" + + install -d "$pkgdir/usr/share/licenses/$pkgname" + ln -s "/usr/lib/R/library/$_pkgname/LICENCE" "$pkgdir/usr/share/licenses/$pkgname" } -# vim:set ts=2 sw=2 et: |